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DOCS: Update sphinx configuration, docs, citations #94

Merged
merged 4 commits into from
Aug 6, 2024
Merged

DOCS: Update sphinx configuration, docs, citations #94

merged 4 commits into from
Aug 6, 2024

Commits on Aug 6, 2024

  1. DOCS: Update sphinx configuration, docs, citations 

    * Adds `.readthedocs.yaml`

* Converts citation to use `BibTex` via the `sphinxcontrib.bibtex`
extension. References are now stored in `docs/references.bib`
and can be cited using `:footcite:`. Citations for each page
will show at the bottom by adding `.. footbibliography::`.

* Adds brief description of `BibTex` citations to `docs/README.md`

* Fixes issues with equation formatting
in `calculations.py` and `diagrams.py`

* Fixes issues with citations in `calculations.py` and `diagrams.py`

* Removes "Kinetic Diagram Analysis" from titles
of main modules (e.g. `calculations.py`)

* Adds `usage.rst` which covers KDA installation
and basic usage, including generating state probabilities
and plotting diagrams

* Updates `index.rst` such that some kinetic
diagrams are rendered on the home page

* Changes `version` and `release` in `conf.py` to
automatically update based on imported `kda` version
    @nawtrey
    nawtrey committed Aug 6, 2024
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  2. Install sphinxcontrib-bibtex from requirements 

    * Add `docs/requirements.txt` with single package
to install, `sphinxcontrib-bibtex`

* Update `readthedocs.yaml` to install
packages from `docs/requirements.txt`
    @nawtrey
    nawtrey committed Aug 6, 2024
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  3. Update docs/requirements.txt 

    * Updates `docs/requirements.txt` in accordance with the
recommendations provided in the following link:
https://docs.readthedocs.io/en/stable/guides/reproducible-
builds.html#use-a-requirements-file-for-python-dependencies
    @nawtrey
    nawtrey committed Aug 6, 2024
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  4. Update docs/requirements.txt 

    * Update `docutils` version to `0.20.1`
for compatibility between `sphinxcontrib-bibtex`
and `sphinx-rtd-theme`
    @nawtrey
    nawtrey committed Aug 6, 2024
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